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- PDB-4whe: Crystal structure of E. coli phage shock protein A (PspA 1-144) -

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Basic information

Entry
Database: PDB / ID: 4whe
TitleCrystal structure of E. coli phage shock protein A (PspA 1-144)
ComponentsPhage shock protein A
KeywordsSIGNALING PROTEIN / PspA/IM30 family / AAA+ protein regulation / transcriptional regulation / stress inducible Psp system / phage shock response / coiled-coil / sigma 54 promoter / transcription initiation
Function / homology
Function and homology information


phage shock / cell pole / regulation of cellular response to stress / phospholipid binding / response to heat / transcription regulator complex / regulation of DNA-templated transcription / identical protein binding / plasma membrane / cytosol
Similarity search - Function
Phage shock protein, PspA / PspA/IM30 / PspA/IM30 family
Similarity search - Domain/homology
Phage shock protein A / Phage shock protein A
Similarity search - Component
Biological speciesEscherichia coli K-12 (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MAD / Resolution: 1.8 Å
AuthorsParthier, C. / Schoepfel, M. / Stubbs, M.T. / Osadnik, H. / Brueser, T.
CitationJournal: Mol.Microbiol. / Year: 2015
Title: PspF-binding domain PspA1-144 and the PspAF complex: New insights into the coiled-coil-dependent regulation of AAA+ proteins.
Authors: Osadnik, H. / Schopfel, M. / Heidrich, E. / Mehner, D. / Lilie, H. / Parthier, C. / Risselada, H.J. / Grubmuller, H. / Stubbs, M.T. / Bruser, T.
History
DepositionSep 22, 2014Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 2, 2015Provider: repository / Type: Initial release
Revision 1.1Nov 18, 2015Group: Database references
Revision 1.2May 8, 2024Group: Data collection / Database references / Category: chem_comp_atom / chem_comp_bond / database_2
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Phage shock protein A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)17,5982
Polymers17,4761
Non-polymers1221
Water1,38777
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area100 Å2
ΔGint2 kcal/mol
Surface area9820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)79.650, 30.377, 80.480
Angle α, β, γ (deg.)90.000, 115.610, 90.000
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-358-

HOH

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Components

#1: Protein Phage shock protein A


Mass: 17476.092 Da / Num. of mol.: 1 / Fragment: UNP residues 1-144
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Escherichia coli K-12 (bacteria) / Gene: pspA, Z2482, ECs1881 / Plasmid: pBAD / Production host: Escherichia coli (E. coli) / Strain (production host): BW25113 / References: UniProt: P0AFM7, UniProt: P0AFM6*PLUS
#2: Chemical ChemComp-TRS / 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL / TRIS BUFFER


Mass: 122.143 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C4H12NO3 / Comment: pH buffer*YM
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 77 / Source method: isolated from a natural source / Formula: H2O

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.64 Å3/Da / Density % sol: 53.36 %
Crystal growTemperature: 288 K / Method: vapor diffusion, hanging drop / pH: 7.2
Details: 0.1 M HEPES/NaOH, 10% (w/v) PEG 6000, 5% (v/v) MPD l

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91841, 0.97981, 0.979927,0.975915
DetectorType: PSI PILATUS 6M / Detector: PIXEL / Date: Jul 16, 2013
RadiationProtocol: MAD / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelength
IDWavelength (Å)Relative weight
10.918411
20.979811
30.9799271
40.9759151
ReflectionNumber: 48941 / Rmerge(I) obs: 0.047 / Χ2: 1.47 / D res high: 2.01 Å / D res low: 39.73 Å / Num. obs: 22364 / % possible obs: 96.7
Diffraction reflection shell
Highest resolution (Å)Lowest resolution (Å)Num. obsIDRmerge(I) obs
5.9639.7382910.018
4.245.96150610.025
3.474.24195510.026
3.013.47233810.037
2.693.01264610.063
2.462.69295810.108
2.282.46316510.161
2.132.28340610.239
2.012.13356110.427
ReflectionResolution: 1.8→39.73 Å / Num. obs: 15969 / % possible obs: 96.8 % / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 37.195 Å2 / Rmerge F obs: 1 / Rmerge(I) obs: 0.031 / Rrim(I) all: 0.037 / Χ2: 0.967 / Net I/σ(I): 20.46 / Num. measured all: 54081
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Highest resolution (Å)Rmerge F obsRmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsRrim(I) all% possible all
1.8-1.90.9290.3983.547875245523470.47495.6
1.9-20.9670.2515.536557195018860.29796.7
2-2.10.9840.1747.575573162915720.20696.5
2.1-2.20.9920.11210.684432133912890.13396.3
2.2-2.660.9970.05817.5112901390937970.06997.1
2.66-3.120.9990.03128.876203193018810.03797.5
3.12-3.580.9990.02143.693764110510790.02597.6
3.58-4.040.9990.01752.6221036486340.02197.8
4.04-4.50.9990.01852.511824073960.02397.3
4.5-100.9990.01955.01318510189860.02396.9
10-2010.01361.0528297900.01692.8
20-3010.00651.192211100.00990.9
3025240

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Phasing

PhasingMethod: MAD

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Processing

Software
NameVersionClassification
Cootmodel building
REFMAC5.8.0069refinement
PDB_EXTRACT3.15data extraction
XSCALEdata scaling
XDSdata reduction
SHELXDphasing
RefinementMethod to determine structure: MAD / Resolution: 1.8→39.73 Å / Cor.coef. Fo:Fc: 0.961 / Cor.coef. Fo:Fc free: 0.929 / WRfactor Rfree: 0.2745 / WRfactor Rwork: 0.2186 / FOM work R set: 0.6813 / SU B: 9.683 / SU ML: 0.141 / SU R Cruickshank DPI: 0.1351 / SU Rfree: 0.138 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.135 / ESU R Free: 0.138 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS U VALUES : WITH TLS ADDED
RfactorNum. reflection% reflectionSelection details
Rfree0.2639 798 5 %RANDOM
Rwork0.2131 15170 --
obs0.2156 15170 96.93 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso max: 172.08 Å2 / Biso mean: 54.663 Å2 / Biso min: 22.09 Å2
Baniso -1Baniso -2Baniso -3
1--3.31 Å20 Å2-0.55 Å2
2--5.98 Å20 Å2
3----1.46 Å2
Refinement stepCycle: final / Resolution: 1.8→39.73 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms1108 0 8 77 1193
Biso mean--71.8 41.79 -
Num. residues----137
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0191141
X-RAY DIFFRACTIONr_bond_other_d0.0010.021191
X-RAY DIFFRACTIONr_angle_refined_deg1.87421530
X-RAY DIFFRACTIONr_angle_other_deg0.90432732
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8495141
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.17424.03557
X-RAY DIFFRACTIONr_dihedral_angle_3_deg16.85615249
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.7851515
X-RAY DIFFRACTIONr_chiral_restr0.1120.2183
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.021248
X-RAY DIFFRACTIONr_gen_planes_other0.0010.02241
X-RAY DIFFRACTIONr_mcbond_it3.1513.327553
X-RAY DIFFRACTIONr_mcbond_other3.133.308551
X-RAY DIFFRACTIONr_mcangle_it4.5064.92688
LS refinement shellResolution: 1.8→1.847 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.376 57 -
Rwork0.362 1086 -
all-1143 -
obs--95.57 %
Refinement TLS params.Method: refined / Details: coil 2 / Origin x: 5.048 Å / Origin y: -1.66 Å / Origin z: 57.218 Å
111213212223313233
T0.0758 Å20.1203 Å2-0.035 Å2-0.2358 Å2-0.1111 Å2--0.0849 Å2
L6.5561 °2-2.5536 °2-1.5148 °2-1.0089 °20.6335 °2--0.818 °2
S0.2715 Å °0.565 Å °-0.2957 Å °-0.0876 Å °-0.2033 Å °0.1201 Å °0.0397 Å °0.1006 Å °-0.0682 Å °

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